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Population genetics
Population genetics is the study of the allele frequency distribution and change under the influence of the four evolutionary processes: natural selection, genetic drift, mutation and gene flow. It also takes account of population subdivision and population structure in space. As such, it attempts to explain such phenomena as adaptation and speciation. Population genetics was a vital ingredient in the modern evolutionary synthesis, its primary founders were Sewall Wright, J. B. S. Haldane and R. A. Fisher, who also laid the foundations for the related discipline of quantitative genetics. Fundamentals Population genetics concerns the genetic constitution of populations and how this constitution changes with time. A population is a localized group of individuals belonging to the same species. For example, all of the moths of the same species living in an isolated forest represent a population. A single gene in this population may have several alternate forms, which account for variations between the phenotypes of the organisms. An example might be a gene for coloration in moths that has two alleles: black and white. A gene pool is the complete set of alleles for a gene in a single population; the allele frequency measures the fraction of the gene pool composed of a single allele (for example, what fraction of moth coloration genes are the black allele). Evolution occurs when there are changes in the frequencies of alleles within a population of interbreeding organisms; for example, the allele for black color in a population of moths becoming more common. To understand the mechanisms that cause a population to evolve, it is useful to consider what conditions are required for a population not to evolve. The Hardy-Weinberg principle states that the frequencies of alleles (variations in a gene) in a sufficiently large population will remain constant if the only forces acting on that population are the random reshuffling of alleles during the formation of the sperm or egg, and the random combination of the alleles in these sex cells during fertilization. Such a population is said to be in Hardy-Weinberg equilibrium; it is not evolving. s: the horizontal axis shows the two allele frequencies p'' and ''q and the vertical axis shows the genotype frequencies. Each graph shows one of the three possible genotypes.]] Hardy–Weinberg principle The Hardy–Weinberg principle states that both allele and genotype frequencies in a population remain constant—that is, they are in equilibrium—from generation to generation unless specific disturbing influences are introduced. Outside the lab, one or more of these "disturbing influences" are always in effect. That is, Hardy Weinberg equilibrium is impossible in nature. Genetic equilibrium is an ideal state that provides a baseline to measure genetic change against. Allele frequencies in a population remain static across generations, provided the following conditions are at hand: random mating, no mutation (the alleles don't change), no migration or emigration (no exchange of alleles between populations), infinitely large population size, and no selective pressure for or against any traits. In the simplest case of a single locus with two alleles: the dominant allele is denoted A''' and the recessive '''a and their frequencies are denoted by p'' and ''q; freq(A') = ''p; freq('''a) = q''; ''p + q'' = 1. If the population is in equilibrium, then we will have freq('AA') = ''p''2 for the '''AA' homozygotes in the population, freq(aa) = q''2 for the '''aa' homozygotes, and freq(Aa) = 2''pq'' for the heterozygotes. Based on these equations, we can determine useful but difficult-to-measure facts about a population. For example, a patient's child is a carrier of a recessive mutation that causes cystic fibrosis in homozygous recessive children. The parent wants to know the probability of her grandchildren inheriting the disease. In order to answer this question, the genetic counselor must know the chance that the child will reproduce with a carrier of the recessive mutation. This fact may not be known, but disease frequency is known. We know that the disease is caused by the homozygous recessive genotype; we can use the Hardy–Weinberg principle to work backward from disease occurrence to the frequency of heterozygous recessive individuals. Scope and theoretical considerations The mathematics of population genetics were originally developed as part of the modern evolutionary synthesis. According to Beatty (1986), for example, it defines the core of the modern synthesis. According to Lewontin (1974) the theoretical task for population genetics is a process in two spaces: a "genotypic space" and a "phenotypic space". The challenge of a complete theory of population genetics is to provide a set of laws that predictably map a population of genotypes (G''1) to a phenotype space (''P''1), where selection takes place, and another set of laws that map the resulting population (''P''2) back to genotype space (''G''2) where Mendelian genetics can predict the next generation of genotypes, thus completing the cycle. Even leaving aside for the moment the non-Mendelian aspects of molecular genetics, this is clearly a gargantuan task. Visualizing this transformation schematically: : G_1 \; \stackrel{T_1}{\rightarrow} \; P_1 \; \stackrel{T_2}{\rightarrow} \; P_2 \; \stackrel{T_3}{\rightarrow} \; G_2 \; \stackrel{T_4}{\rightarrow} \; G_1' \; \rightarrow \cdots (adapted from Lewontin 1974, p. 12). XD ''T''1 represents the genetic and epigenetic laws, the aspects of functional biology, or development, that transform a genotype into phenotype. We will refer to this as the "genotype-phenotype map". ''T''2 is the transformation due to natural selection, ''T''3 are epigenetic relations that predict genotypes based on the selected phenotypes and finally ''T''4 the rules of Mendelian genetics. In practice, there are two bodies of evolutionary theory that exist in parallel, traditional population genetics operating in the genotype space and the biometric theory used in plant and animal breeding, operating in phenotype space. The missing part is the mapping between the genotype and phenotype space. This leads to a "sleight of hand" (as Lewontin terms it) whereby variables in the equations of one domain, are considered parameters or ''constants, where, in a full-treatment they would be transformed themselves by the evolutionary process and are in reality functions of the state variables in the other domain. The "sleight of hand" is assuming that we know this mapping. Proceeding as if we do understand it is enough to analyze many cases of interest. For example, if the phenotype is almost one-to-one with genotype (sickle-cell disease) or the time-scale is sufficiently short, the "constants" can be treated as such; however, there are many situations where it is inaccurate. The four processes Natural selection Natural selection is the process by which heritable traits that make it more likely for an organism to survive and successfully reproduce become more common in a population over successive generations. The natural genetic variation within a population of organisms means that some individuals will survive more successfully than others in their current environment. Factors which affect reproductive success are also important, an issue which Charles Darwin developed in his ideas on sexual selection. Natural selection acts on the phenotype, or the observable characteristics of an organism, but the genetic (heritable) basis of any phenotype which gives a reproductive advantage will become more common in a population (see allele frequency). Over time, this process can result in adaptations that specialize organisms for particular ecological niches and may eventually result in the emergence of new species. Natural selection is one of the cornerstones of modern biology. The term was introduced by Darwin in his groundbreaking 1859 book On the Origin of Species, Darwin C (1859) On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life John Murray, London; modern reprint Published online at The complete work of Charles Darwin online: On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. in which natural selection was described by analogy to artificial selection, a process by which animals and plants with traits considered desirable by human breeders are systematically favored for reproduction. The concept of natural selection was originally developed in the absence of a valid theory of heredity; at the time of Darwin's writing, nothing was known of modern genetics. The union of traditional Darwinian evolution with subsequent discoveries in classical and molecular genetics is termed the modern evolutionary synthesis. Natural selection remains the primary explanation for adaptive evolution. Genetic drift Genetic drift is the change in the relative frequency in which a gene variant (allele) occurs in a population due to random sampling and chance: The alleles in offspring are a random sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces. A population's allele frequency is the fraction of the gene copies that share a particular form. Genetic drift is an important evolutionary process which leads to changes in allele frequencies over time. It may cause gene variants to disappear completely, and thereby reduce genetic variability. In contrast to natural selection, which makes gene variants more common or less common depending on their reproductive success, the changes due to genetic drift are not driven by environmental or adaptive pressures, and may be beneficial, neutral, or detrimental to reproductive success. The effect of genetic drift is larger in small populations, and smaller in large populations. Vigorous debates wage among scientists over the relative importance of genetic drift compared with natural selection. Ronald Fisher held the view that genetic drift plays at the most a minor role in evolution, and this remained the dominant view for several decades. In 1968 Motoo Kimura rekindled the debate with his neutral theory of molecular evolution which claims that most of the changes in the genetic material are caused by genetic drift. Mutation Mutations are changes in the DNA sequence of a cell's genome and are caused by radiation, viruses, transposons and mutagenic chemicals, as well as errors that occur during meiosis or DNA replication. Errors are introduced particularly often in the process of DNA replication, in the polymerization of the second strand. These errors. They can also be induced by the organism itself, by cellular processes such as hypermutation. Mutations can have an impact on the phenotype of an organism, especially if they occur within the protein coding sequence of a gene. Error rates are usually very low—1 error in every 10 million–100 million bases—due to the "proofreading" ability of DNA polymerases. Without proofreading, error rates are a thousand-fold higher. Chemical damage to DNA occurs naturally as well, and cells use DNA repair mechanisms to repair mismatches and breaks in DNA. Nevertheless, the repair sometimes fails to return the DNA to its original sequence. In organisms that use chromosomal crossover to exchange DNA and recombine genes, errors in alignment during meiosis can also cause mutations. Errors in crossover are especially likely when similar sequences cause partner chromosomes to adopt a mistaken alignment; this makes some regions in genomes more prone to mutating in this way. These errors create large structural changes in DNA sequence—duplications, inversions or deletions of entire regions, or the accidental exchanging of whole parts between different chromosomes (called translocation). Mutation can result in several different types of change in DNA sequences; these can either have no effect, alter the product of a gene, or prevent the gene from functioning. Studies in the fly Drosophila melanogaster suggest that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70 percent of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial. Due to the damaging effects that mutations can have on cells, organisms have evolved mechanisms such as DNA repair to remove mutations. Therefore, the optimal mutation rate for a species is a trade-off between costs of a high mutation rate, such as deleterious mutations, and the metabolic costs of maintaining systems to reduce the mutation rate, such as DNA repair enzymes. Viruses that use RNA as their genetic material have rapid mutation rates, which can be an advantage since these viruses will evolve constantly and rapidly, and thus evade the defensive responses of e.g. the human immune system. Mutations can involve large sections of DNA becoming duplicated, usually through genetic recombination. These duplications are a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in animal genomes every million years. Most genes belong to larger families of genes of shared ancestry. Novel genes are produced by several methods, commonly through the duplication and mutation of an ancestral gene, or by recombining parts of different genes to form new combinations with new functions. Here, domains act as modules, each with a particular and independent function, that can be mixed together to produce genes encoding new proteins with novel properties. For example, the human eye uses four genes to make structures that sense light: three for color vision and one for night vision; all four arose from a single ancestral gene. Another advantage of duplicating a gene (or even an entire genome) is that this increases redundancy; this allows one gene in the pair to acquire a new function while the other copy performs the original function. Other types of mutation occasionally create new genes from previously noncoding DNA. Gene flow Gene flow is the exchange of genes between populations, which are usually of the same species. Examples of gene flow within a species include the migration and then breeding of organisms, or the exchange of pollen. Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer. Migration into or out of a population can change allele frequencies, as well as introducing genetic variation into a population. Immigration may add new genetic material to the established gene pool of a population. Conversely, emigration may remove genetic material. As barriers to reproduction between two diverging populations are required for the populations to become new species, gene flow may slow this process by spreading genetic differences between the populations. Gene flow is hindered by mountain ranges, oceans and deserts or even man-made structures such as the Great Wall of China, which has hindered the flow of plant genes. Depending on how far two species have diverged since their most recent common ancestor, it may still be possible for them to produce offspring, as with horses and donkeys mating to produce mules. Such hybrids are generally infertile, due to the two different sets of chromosomes being unable to pair up during meiosis. In this case, closely related species may regularly interbreed, but hybrids will be selected against and the species will remain distinct. However, viable hybrids are occasionally formed and these new species can either have properties intermediate between their parent species, or possess a totally new phenotype. The importance of hybridization in creating new species of animals is unclear, although cases have been seen in many types of animals, with the gray tree frog being a particularly well-studied example. Hybridization is, however, an important means of speciation in plants, since polyploidy (having more than two copies of each chromosome) is tolerated in plants more readily than in animals. Polyploidy is important in hybrids as it allows reproduction, with the two different sets of chromosomes each being able to pair with an identical partner during meiosis. Polyploids also have more genetic diversity, which allows them to avoid inbreeding depression in small populations. Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring; this is most common among bacteria. In medicine, this contributes to the spread of antibiotic resistance, as when one bacteria acquires resistance genes it can rapidly transfer them to other species. Horizontal transfer of genes from bacteria to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean beetle Callosobruchus chinensis may also have occurred. An example of larger-scale transfers are the eukaryotic bdelloid rotifers, which appear to have received a range of genes from bacteria, fungi, and plants. Viruses can also carry DNA between organisms, allowing transfer of genes even across biological domains. Large-scale gene transfer has also occurred between the ancestors of eukaryotic cells and prokaryotes, during the acquisition of chloroplasts and mitochondria. Gene flow is the transfer of alleles from one population to another. Migration into or out of a population may be responsible for a marked change in allele frequencies. Immigration may also result in the addition of new genetic variants to the established gene pool of a particular species or population. There are a number of factors that affect the rate of gene flow between different populations. One of the most significant factors is mobility, as greater mobility of an individual tends to give it greater migratory potential. Animals tend to be more mobile than plants, although pollen and seeds may be carried great distances by animals or wind. Maintained gene flow between two populations can also lead to a combination of the two gene pools, reducing the genetic variation between the two groups. It is for this reason that gene flow strongly acts against speciation, by recombining the gene pools of the groups, and thus, repairing the developing differences in genetic variation that would have led to full speciation and creation of daughter species. For example, if a species of grass grows on both sides of a highway, pollen is likely to be transported from one side to the other and vice versa. If this pollen is able to fertilise the plant where it ends up and produce viable offspring, then the alleles in the pollen have effectively been able to move from the population on one side of the highway to the other. Genetic structure Because of physical barriers to migration, along with limited vagility, and natal philopatry, natural populations are rarely panmictic (Buston et al., 2007). There is usually a geographic range within which individuals are more closely related to one another than those randomly selected from the general population. This is described as the extent to which a population is genetically structured (Repaci et al., 2007). Microbial population genetics Microbial population genetics is a rapidly advancing field of investigation with relevance to many other theoretical and applied areas of scientific investigations. The population genetics of microorganisms lays the foundations for tracking the origin and evolution of antibiotic resistance and deadly infectious pathogens. Population genetics of microorganisms is also an essential factor for devising strategies for the conservation and better utilization of beneficial microbes (Xu, 2010). History Population genetics The Mendelian and biometrician models were eventually reconciled, when population genetics] was developed. A key step was the work of the British biologist and statistician R.A. Fisher. In a series of papers starting in 1918 and culminating in his 1930 book The Genetical Theory of Natural Selection, Fisher showed that the continuous variation measured by the biometricians could be produced by the combined action of many discrete genes, and that natural selection could change gene frequencies in a population, resulting in evolution. In a series of papers beginning in 1924, another British geneticist, J.B.S. Haldane, applied statistical analysis to real-world examples of natural selection, such as the evolution of industrial melanism in peppered moths, and showed that natural selection worked at an even faster rate than Fisher assumed. The American biologist Sewall Wright, who had a background in animal breeding experiments, focused on combinations of interacting genes, and the effects of inbreeding on small, relatively isolated populations that exhibited genetic drift. In 1932, Wright introduced the concept of an adaptive landscape and argued that genetic drift and inbreeding could drive a small, isolated sub-population away from an adaptive peak, allowing natural selection to drive it towards different adaptive peaks. Fisher and Wright had some fundamental disagreements and a controversy about the relative roles of selection and drift continued for much of the century between the Americans and the British. The Frenchman Gustave Malécot was also important early in the development of the discipline. The work of Fisher, Haldane and Wright founded the discipline of population genetics. This integrated natural selection with Mendelian genetics, which was the critical first step in developing a unified theory of how evolution worked. John Maynard Smith was Haldane's pupil, whilst W.D. Hamilton was heavily influenced by the writings of Fisher. The American George R. Price worked with both Hamilton and Maynard Smith. American Richard Lewontin and Japanese Motoo Kimura were heavily influenced by Wright. Modern evolutionary synthesis In the first few decades of the 20th century, most field naturalists continued to believe that Lamarckian and orthogenic mechanisms of evolution provided the best explanation for the complexity they observed in the living world. However, as the field of genetics continued to develop, those views became less tenable. Theodosius Dobzhansky, a postdoctoral worker in T. H. Morgan's lab, had been influenced by the work on genetic diversity by Russian geneticists such as Sergei Chetverikov. He helped to bridge the divide between the foundations of microevolution developed by the population geneticists and the patterns of macroevolution observed by field biologists, with his 1937 book Genetics and the Origin of Species. Dobzhansky examined the genetic diversity of wild populations and showed that, contrary to the assumptions of the population geneticists, these populations had large amounts of genetic diversity, with marked differences between sub-populations. The book also took the highly mathematical work of the population geneticists and put it into a more accessible form. In Great Britain E.B. Ford, the pioneer of ecological genetics, continued throughout the 1930s and 1940s to demonstrate the power of selection due to ecological factors including the ability to maintain genetic diversity through genetic polymorphisms such as human blood types. Ford's work would contribute to a shift in emphasis during the course of the modern synthesis towards natural selection over genetic drift. See also * Assortative mating * Behavioral genetics * Coalescent theory * Dual inheritance theory * Ecological genetics * Evolutionarily Significant Unit * Ewens's sampling formula * Fitness landscape * Founder effect * Genetic diversity * Genetic drift * Genetic erosion * Genetic engineering * Genetic pollution * Gene pool * Genotype-phenotype distinction * Habitat fragmentation * Hardy-Weinberg principle * Microevolution * Molecular evolution * Muller's ratchet * Mutational meltdown * Neutral theory of molecular evolution * Population bottleneck * Quantitative genetics * Reproductive compensation * Selection * Small population size References * J. Beatty. "The synthesis and the synthetic theory" in Integrating Scientific Disciplines, edited by W. Bechtel and Nijhoff. Dordrecht, 1986. * * Luigi Luca Cavalli-Sforza. Genes, Peoples, and Languages. North Point Press, 2000. * Luigi Luca Cavalli-Sforza et al. The History and Geography of Human Genes. Princeton University Press, 1994. * James F. Crow and Motoo Kimura. Introduction to Population Genetics Theory. Harper & Row, 1972. * Warren J Ewens. Mathematical Population Genetics. Springer-Verlag New York, Inc., 2004. ISBN 0-387-20191-2 * John H. Gillespie Population Genetics: A Concise Guide, Johns Hopkins Press, 1998. ISBN 0-8018-5755-4. * Richard Halliburton. Introduction to Population Genetics. Prentice Hall, 2004 * Daniel Hartl. Primer of Population Genetics, 3rd edition. Sinauer, 2000. ISBN 0-87893-304-2 * Daniel Hartl and Andrew Clark. Principles of Population Genetics, 3rd edition. Sinauer, 1997. ISBN 0-87893-306-9. * Richard C. Lewontin. The Genetic Basis of Evolutionary Change. Columbia University Press, 1974. * William B. Provine. The Origins of Theoretical Population Genetics. University of Chicago Press. 1971. ISBN 0-226-68464-4. * * Spencer Wells. The Journey of Man. Random House, 2002. * Spencer Wells. Deep Ancestry: Inside the Genographic Project. National Geographic Society, 2006. * * Xu, J. Microbial Population Genetics. Caister Academic Press, 2010. ISBN 978-1-904455-59-2 External links * Yale University * EHSTRAFD.org - Earth Human STR Allele Frequencies Database * History of population genetics * National Geographic: Atlas of the Human Journey (Haplogroup-based human migration maps) * Monash Virtual Laboratory - Simulations of habitat fragmentation and population genetics online at Monash University's Virtual Laboratory. * Nordic and Celtic DNA Project (Saami & Iberian). Category:Genetics * Category:Evolutionary biology Category:Statistical genetics